The half-hour The Secret Squirrel Show included three individual cartoon segments: "Secret Squirrel", "Squiddly Diddly" and "Winsome Witch".
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| Title | Air Date | Duration | ||
|---|---|---|---|---|
| Season 1 | Episode 1 | Yellow Pinkie | 1965-10-02 | 7 min |
| Season 1 | Episode 2 | Wolf in Cheap Cheap Clothing | 1965-10-09 | 7 min |
| Season 1 | Episode 3 | Scotland Yard Caper | 1965-10-16 | 7 min |
| Season 1 | Episode 4 | Sub Swiper | 1965-10-23 | 7 min |
| Season 1 | Episode 5 | Royal Run Around | 1965-10-30 | 7 min |
| Season 1 | Episode 6 | Masked Granny | 1965-11-06 | 7 min |
| Season 1 | Episode 7 | Robin Hood and His Merry Muggs | 1965-11-13 | 7 min |
| Season 1 | Episode 8 | Five is a Crowd | 1965-11-20 | 7 min |
| Season 1 | Episode 9 | It Stopped Training | 1965-11-27 | 7 min |
| Season 1 | Episode 10 | Wacky Secret Weapon | 1965-12-04 | 7 min |
| Season 1 | Episode 11 | Cuckoo Clock Cuckoo | 1965-12-11 | 7 min |
| Season 1 | Episode 12 | Catty Cornered | 1965-12-18 | 7 min |
| Season 1 | Episode 13 | Leave Wheel Enough Alone | 1965-12-25 | 7 min |
| Season 2 | Episode 1 | Jester Minute | 1966-01-01 | 7 min |
| Season 2 | Episode 2 | Not So Idle Idol | 1966-01-08 | 7 min |
| Season 2 | Episode 3 | Gold Rushed | 1966-01-15 | 7 min |
| Season 2 | Episode 4 | Double Ex-Double Cross | 1966-01-22 | 7 min |
| Season 2 | Episode 5 | Capt. Kidd's Not Kidding | 1966-01-29 | 7 min |
| Season 2 | Episode 6 | Tusk-Tusk | 1966-02-05 | 7 min |
| Season 2 | Episode 7 | Bold Rush | 1966-02-12 | 7 min |
| Season 2 | Episode 8 | Robot Rout | 1966-02-19 | 7 min |
| Season 2 | Episode 9 | Hi Spy | 1966-02-26 | 7 min |
| Season 2 | Episode 10 | The Pink Sky Mobile | 1966-03-05 | 7 min |
| Season 2 | Episode 11 | Scuba-Duba Duba | 1966-03-12 | 7 min |
| Season 2 | Episode 12 | Spy in the Sky | 1966-03-19 | 7 min |
| Season 2 | Episode 13 | Ship of Spies | 1966-03-26 | 7 min |
| Directing | William Hanna | Director |
| Directing | Joseph Barbera | Director |
